Chronic kidney disease (CKD) is a common condition among elderly patients and has been reported to be a biomarker for the presence of malignant disease. In addition, unfavorable outcomes for patients with upper tract urothelial carcinoma (UTUC) undergoing radical nephroureterectomy can be due to independent clinical factors. Therefore, the present study analyzed the clinicopathological data of patients with UTUC, who underwent radical nephroureterectomy at our institution, to clarify whether preoperative CKD and other factors are independent predictors of the shorter disease-specific and/or recurrence-free survival time of these patients. A retrospective review of 187 patients who underwent radical nephroureterectomy was conducted, and patients were followed for at least 3 months postoperatively. The clinicopathological factors that are thought to have potentially significant roles in the progression and metastasis of malignant tumors and for disease-specific and recurrence-free survival were evaluated. Positive surgical margins and an estimation of the glomerular filtration rate (eGFR) of <60 were independent factors for the shorter disease-specific survival time in multivariate analysis with Cox's proportional hazards model [hazard ratio (HR), 2.401: 95% confidence interval (CI), 1.044-5.255; and HR, 2.371: 95% CI, 1.024-5.898, respectively]. Another multivariate analysis also revealed that positive surgical margins (HR, 4.477; 95% CI, 2.042-9.469), and preoperative eGFR <60 (HR, 2.362; 95% CI, 1.067-5.592) were independent factors for the worse recurrence-free survival rate in all patients. Patients with UTUC who had eGFR <60 as well as positive surgical margins had significantly shorter time to disease-specific mortality and extraurothelial recurrence. The present study demonstrated that patients with UTUC undergoing radical nephroureterectomy who have CKD as well as positive surgical margins should be carefully followed up postoperatively.